From 8ffdf33ae5013917cdce00c0e4ffaf92cc70e204 Mon Sep 17 00:00:00 2001
From: sharoncy <s.c.yates@medisin.uio.no>
Date: Wed, 3 Apr 2024 12:58:59 +0200
Subject: [PATCH] Fix colour "auto"
---
PyNutil/coordinate_extraction.py | 6 +++---
test/test10_PyNutil_web.json | 2 +-
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/PyNutil/coordinate_extraction.py b/PyNutil/coordinate_extraction.py
index a58ae14..a459c06 100644
--- a/PyNutil/coordinate_extraction.py
+++ b/PyNutil/coordinate_extraction.py
@@ -243,13 +243,13 @@ def load_segmentation(segmentation_path: str):
else:
return cv2.imread(segmentation_path)
-def remove_background(segmentation: np.array):
+def detect_pixel_id(segmentation: np.array):
"""Remove the background from the segmentation and return the pixel id."""
segmentation_no_background = segmentation[~np.all(segmentation == 0, axis=2)]
print("length of non background pixels: ", len(segmentation_no_background))
pixel_id = segmentation_no_background[0]
print("detected pixel_id: ", pixel_id)
- return segmentation_no_background, pixel_id
+ return pixel_id
def get_region_areas(use_flat, atlas_labels, flat_file_atlas, seg_width, seg_height, slice_dict, atlas_volume, triangulation):
if use_flat:
@@ -299,7 +299,7 @@ def segmentation_to_atlas_space(
):
segmentation = load_segmentation(segmentation_path)
if pixel_id == "auto":
- segmentation, pixel_id = remove_background(segmentation)
+ pixel_id = detect_pixel_id(segmentation)
seg_height, seg_width = segmentation.shape[:2]
reg_height, reg_width = slice_dict["height"], slice_dict["width"]
if non_linear and "markers" in slice_dict:
diff --git a/test/test10_PyNutil_web.json b/test/test10_PyNutil_web.json
index 81a2f91..fd8a95a 100644
--- a/test/test10_PyNutil_web.json
+++ b/test/test10_PyNutil_web.json
@@ -4,6 +4,6 @@
"segmentation_folder": "PyNutil/test_data/PyTest_web",
"alignment_json": "PyNutil/test_data/PyNutil_test.waln",
"nonlinear": true,
- "colour": [0, 0, 0],
+ "colour": "auto",
"points_json_path": "PyNutil/outputs/test.json"
}
--
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